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IPB Newsletter | April 2025
Understanding Plants!

The IPB Video
Molecular Signal Processing

Prof. Dr. Steffen Abel
How plants stand their ground.
Bioorganic Chemistry

Prof. Dr. Ludger Wessjohann
The chemistry of nature - basis for active compounds for human and plant health.
Biochemistry of Plant Interactions

Prof. Dr. Tina Romeis
Interactions in, of and with plants.
Cell and Metabolic Biology

Prof. Dr. Alain Tissier
Secondary but never unimportant - the biological functions of plant secondary metabolites.
Independent Junior Research Group

Dr. Mariana Schuster

New findings on OPDA: No signaling effect in the early wound response

The plant stress hormone jasmonic acid (JA) and its bioactive form jasmonoyl isoleucine (JA-Ile) play a central role in the…

The IPB has once again been recognized for its exemplary actions in terms of equal opportunity-oriented personnel and organizational policies and has received the TOTAL E-QUALITY certification for the…

The Plant Science Student Conference (PSSC) has been organised by students from the two Leibniz institutes, IPK and IPB, every year for the last 20 years. In this interview, Christina Wäsch (IPK) and…

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Synthetic Organic Chemist (m/f/d) (18/2025)

Date: 2025-08-19 Reference Number: 18/2025

PhD position in biology (m/f/d) (17/2025)

Date: 2025-08-08 Reference Number: 17/2025

PhD in Machine Learning for Enzyme Design (m/f/d)

Date: 2025-05-16 Reference Number: 11/2025

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Gonzalez-Beltran, A.; Neumann, S.; Maguire, E.; Sansone, S.-A.; Rocca-Serra, P.; The Risa R/Bioconductor package: integrative data analysis from experimental metadata and back again BMC Bioinformatics 15 (Suppl 1) S11 (2014) DOI: 10.1186/1471-2105-15-S1-S11

BackgroundThe ISA-Tab format and software suite have been developed to break the silo effect induced by technology-specific formats for a variety of data types and to better support experimental metadata tracking. Experimentalists seldom use a single technique to monitor biological signals. Providing a multi-purpose, pragmatic and accessible format that abstracts away common constructs for describing I nvestigations, S tudies and A ssays, ISA is increasingly popular. To attract further interest towards the format and extend support to ensure reproducible research and reusable data, we present the Risa package, which delivers a central component to support the ISA format by enabling effortless integration with R, the popular, open source data crunching environment.ResultsThe Risa package bridges the gap between the metadata collection and curation in an ISA-compliant way and the data analysis using the widely used statistical computing environment R. The package offers functionality for: i) parsing ISA-Tab datasets into R objects, ii) augmenting annotation with extra metadata not explicitly stated in the ISA syntax; iii) interfacing with domain specific R packages iv) suggesting potentially useful R packages available in Bioconductor for subsequent processing of the experimental data described in the ISA format; and finally v) saving back to ISA-Tab files augmented with analysis specific metadata from R. We demonstrate these features by presenting use cases for mass spectrometry data and DNA microarray data.ConclusionsThe Risa package is open source (with LGPL license) and freely available through Bioconductor. By making Risa available, we aim to facilitate the task of processing experimental data, encouraging a uniform representation of experimental information and results while delivering tools for ensuring traceability and provenance tracking.Software availabilityThe Risa package is available since Bioconductor 2.11 (version 1.0.0) and version 1.2.1 appeared in Bioconductor 2.12, both along with documentation and examples. The latest version of the code is at the development branch in Bioconductor and can also be accessed from GitHub https://github.com/ISA-tools/Risa, where the issue tracker allows users to report bugs or feature requests.

IPB Newsletter | April 2025

Understanding Plants!

Molecular Signal Processing

Bioorganic Chemistry

Biochemistry of Plant Interactions

Cell and Metabolic Biology

Independent Junior Research Group

+++ News Ticker Science 183 +++ Phytohormones +++

New findings on OPDA: No signaling effect in the early wound response

IPB receives TOTAL E-QUALITY certification for the sixth time in a row

PSSC: Success for the ‘Iron Lady’

Synthetic Organic Chemist (m/f/d) (18/2025)

PhD position in biology (m/f/d) (17/2025)

PhD in Machine Learning for Enzyme Design (m/f/d)

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